I reduced the scope of this question to prevent it being closed as too broad, and to match the only answer. To ask the same question for another product just ask a new question.
– PolyGeo♦Apr 25 '17 at 20:35

Thanks - how? I've opened the plugin, do I need to add a rule of some kind? I've tried adding one saying that my layer is layer #1 and it "must not overlap", with no layer #2 - is that what you mean? It's running, but is very slow because my layer is large, so I'm not sure what it will find.
– RichardApr 25 '17 at 15:38